178
Opinion
TRENDS in Biochemical Sciences Vol.27 No.4 April 2002
Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding Guillaume Stahl, Gregory P. McCarty and Philip J. Farabaugh The ribosome is a molecular machine that converts genetic information in the form of RNA, into protein. Recent structural studies reveal a complex set of interactions between the ribosome and its ligands, mRNA and tRNA, that indicate ways in which the ribosome could avoid costly translational errors. Ribosomes must decode each successive codon accurately, and structural data provide a clear indication of how ribosomes limit recruitment of the wrong tRNA (sense errors). In a triplet-based genetic code there are three potential forward reading frames, only one of which encodes the correct protein. Errors in which the ribosome reads a codon out of the normal reading frame (frameshift errors) occur less frequently than sense errors, although it is not clear from structural data how these errors are avoided. Some mRNA sequences, termed programmed-frameshift sites, cause the ribosome to change reading frame. Based on recent work on these sites, this article proposes that the ribosome uses the structure of the codon–anticodon complex formed by the peptidyl-tRNA, especially its wobble interaction, to constrain the incoming aminoacyl-tRNA to the correct reading frame.
Guillaume Stahl Gregory P. McCarty Philip J. Farabaugh* Dept of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland, Baltimore County, Baltimore, MD 21250, USA. *e-mail: farabaug@ umbc.edu
Arguably the most important feature of protein synthesis is the ability to maintain the correct reading frame. When reading an mRNA, a ribosome must correctly interpret each successive tri-nucleotide codon as a particular amino acid. The ribosome must also decode only adjacent, nonoverlapping codons – those lying in a single reading frame. However, mRNA lacks punctuation, internal signals that identify which nucleotide triplets constitute codons (first noted by Crick et al. [1]). Therefore, when a ribosome loses track of the correct reading frame it has no way to re-establish this. Although ribosomes do make frameshift errors, these occur at a very low rate, probably much less than 5 × 10−5 per codon, or at least an order of magnitude less frequently than ribosomes incorporate an incorrect amino acid (termed sense errors) [2]. Although we lack an explicit, accepted model for frame maintenance, we do have a more complete http://tibs.trends.com
understanding about the correction of sense errors. The error-correction machinery distinguishes between correct (cognate) and incorrect (noncognate) aminoacyl-tRNAs (aa-tRNAs) by the structures they form in the decoding sites. Ribosomes increase the accuracy of tRNA recruitment and recognition by a process called kinetic proofreading [3–5]. To amplify discrimination, the process of tRNA selection is divided into two steps, one before and one after GTP hydrolysis, by elongation factor Tu (EF-Tu), which deposits aa-tRNA onto the ribosome. During each step, noncognate tRNA is much more likely to dissociate from the ribosome than is cognate tRNA. Moreover, recent observations show that when bound to the ribosome, cognate complexes formed between aa-tRNA and EF-Tu manipulate the ribosome and improve discrimination [6–8]. The past two years have witnessed an incredible burst of information about the structure of the ribosome and its interactions with ligands. For our purposes, the precise nature of the interaction between the mRNA, tRNAs and the 30S ribosome are most exciting [9–11]. The data give a glimpse of the workings of this amazing molecular machine; in particular, a clearer picture of the nature of the errorcorrection process. Ribosomes have three tRNAbinding sites, termed aminoacyl (A), peptidyl (P) and exit (E) sites. During translation, aa-tRNAs enter the ribosome and bind to a codon in the A site. After accepting transfer of the growing peptide from the preceding tRNA, they translocate to the P site, donate the peptide to the succeeding tRNA and move to the E site before dissociating from the ribosome. The newly available structures confirm that tRNA basepairs with the mRNA in the A- and P sites, and show that nucleotides and amino acids in the ribosome directly contact the codon–anticodon complex in each site (Fig. 1). A description of the interactions in the A site comes from Ogle et al. [9], who solved a structure of the 30S subunit complexed with models of the mRNA and A-site tRNA to
